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| [[WormBase-Caltech_Weekly_Calls_July_2016|July]] | | [[WormBase-Caltech_Weekly_Calls_July_2016|July]] |
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− | | + | [[WormBase-Caltech_Weekly_Calls_August_2016|August]] |
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− | == August 4, 2016 ==
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− | === Parasite Paper Pipeline and Curation Status Tracking ===
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− | *~4% of Journal articles (roughly, but not precisely, translates to curatable papers) mention both Caenorhabditis species and parasite species
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− | *We discussed last week the options for accurately tracking data type flagging and curation status for these papers
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− | *SVM does not flag data at the species level, but we need a way to distinguish curation status based on species or it will be difficult to get accurate numbers for Caltech and Hinxton
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− | *One option would be to have separate status tables
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− | **Lump Caltech and Hinxton species together or distinguish each species separately?
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− | *Other options?
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− | === Intellectual lineage graph ===
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− | * Raymond - are we ready to implement as a widget on person page?
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− | * Can toggle to show only direct relationships
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− | * Will eventually be able to toggle by relationship type
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− | * These will simplify complex graphs
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− | === SVM for MGI ===
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− | * Yuling is tying up loose ends for MGI SVM before he leaves
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− | === AGR Timeline meeting ===
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− | * Timeline still pretty high-level but making progress
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− | === Complex genotype to phenotype annotation ===
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− | * Chris - still planning to work out details over models mailing list
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− | * We can go ahead with the creation of phenotype report objects to encapsulate complex genotypes
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− | * Another approach to consider is whether or not to create "set" objects that contain sets of, for example, alleles, genes, etc.
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− | * We could potentially reuse sets as they come up again in different contexts, or in replicate experiments
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− | | |
− | === Teleconference line ===
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− | * New AT&T conference call is OK, not great
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− | * BlueJeans is too expensive for our purposes
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− | == August 11, 2016 ==
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− | === Micropublications ===
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− | * Would like to make more prominent on homepage
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− | * Expanding micropublications to phenotype
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− | ** Would we require images, photographs of mutant worms
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− | ** Can clone phenotype form, but remove requirement for publication; also add funding sources
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− | ** Would negative data require controls?
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− | == August 18, 2016 ==
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− | === Citace local upload August 30 ===
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− | === Tazendra ===
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− | * Raymond installing new network card
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− | * Recent network crashes, unclear why
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− | * Raymond sent a help desk ticket to IMSS; no response so far
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− | * Michael and Ranjana have gotten network errors as well (when trying to deal with automated descriptions)
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− | | |
− | === Models updating ===
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− | * Wen has GitHub page bookmarked to retrieve latest models.wrm file
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− | * Older CVS system had used explicit release ID in name of file; not same now with GitHub
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− | * With GitHub, it could be easy to script retrieval of latest models.wrm file
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− | === Anatomy ontology, from OBO to OWL ===
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− | * Major reason to do it: make direct connections to terms in other ontologies
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− | * Can take advantage of other anatomy ontologies
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− | * Should the WBbt "cell" be synonymous with generic "cell" or be referred to as "C. elegans cell"?
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− | * Import versus cross-reference approach to linking ontologies
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− | === Noctua, LEGO curation ===
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− | * Weekly meetings, Monday mornings
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− | * Nearly ready to release Noctua for use
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− | * Ongoing discussion about use of relations from the relations ontology; maybe need some new terms
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− | * Idea is to make Noctua the main GO annotation tool, for simple or complex annotations
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− | * People still using legacy GAF file, need to transition to OWL format
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− | * Training session at end of month (next week)
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− | * GO meeting at USC in November; will dedicate the following week to Noctua/LEGO training workshop (Monday Nov 7th?)
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− | * While curating need to consider whether a molecular function regulates a process or is part of a process; requires explicit positioning
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− | * Need to deal with annotations to a generic gene product versus a specific gene product (one or all isoforms, for example)
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− | * Would want a "enabled by product of" relation for genes
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− | * Chris M concerned with having too many relations for curators to know/keep track of
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− | * Training material should be available from the Noctua homepage
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− | === Community Phenotype annotation ===
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− | * Still sending out emails, reached stopping point, for now (emailed most authors within last month)
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− | * Still getting consistent responses from authors
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− | * Working on homepage widget to display top contributors
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− | === Micropublications ===
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− | * Daniela had sent out solicitations for expression data; some people expressed interest, but haven't heard back
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− | * We could take the phenotype form and modify for micropublication
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